Barrier removal and dynamics of intermittent stream habitat regulate persistence and structure of fish community

Barrier effects observed in the presence of weirs are exacerbated by low water levels. We conducted a 10-year study to assess the ecological effects of stream restoration while analysing the possibility of a seasonal lack of hydrological continuity, with multiple measurements before and after restoring stream structural continuity. The research hypothesis assumes that in intermittent streams, there would be little or no change in the fish community downstream the barrier before vs. after barrier removal, and a significant change upstream the barrier before vs. after. Our results indicate, that by removing small barriers, their detrimental effects on the longitudinal passage of riverine fishes and fish assemblages can be rehabilitated. In the wet season, fish migrants from the mainstem river appeared in the downstream section of the stream. Stream intermittency, however, placed a habitat filter over the assemblage. Thus, after barrier removal, only two small-bodied fish species that tolerate periodic oxygen deficiencies and rising water temperatures gradually shifted upstream and formed stable populations. We emphasize, that we should not refrain from restoring the longitudinal continuity of intermittent streams, because they periodically provide fish valuable refugia and can also be a source of new generations and strengthen fish populations in mainstem river.

. Pair-wise tests results from PERMANOVA of the fish assemblages at sites in two reaches the Hołubla Stream Table A2. Species-age classis contributing of the similarity in the fish communities within each of the three groups of sites (one-way SIMPER analysis). Table A3. Additional information -detailed study area characteristics.        Table A2. Species-age classis contributing of the similarity in the fish communities within each of the three groups of sites (one-way SIMPER analysis). 0,07 0,01 0,08 0,03 100,00 Each species contribution (Con) to the total similarity within the site is given as a percentage, and the cumulative contribution (CuCon) of each taxon. Column 5 gives the ratio of average similarity (AvSim) divided by standard deviation (SD); Average abundance, log(x+1) transformed (AvAbu);

Detailed study area characteristics a)
• The section of the San River downstream the mouth of the Hołubla Stream is largely regulated.
• Modifications of the San River channel were implemented from the second half of the 19th century, and these modifications covered, among others, the ~70-km reach of the river, located approximately 15 km downstream of the mouth of the Hołubla Stream. • In this section, the meanders along the river were removed to make the river straighter; thus, the San River has been shortened by almost 40 km. Consequently, there has been more than a twofold increase in the slope of the riverbed; the San River channel cut into alluvial deposits and the riverbed bottom was lowered by almost 4 m (Dynowska and Maciejewski, 1991).  Table A4). • The summer months were warm, very warm, or extremely warm (Table A3; IMWM, 2020).
• Individual springs in the research period 2010-2019 were defined as dry, normal, or wet (Table  A3). Consequently, the FLOW (spring) and DRY (summer) states were distinguished in each year.  (Table A4, A5). • In the middle course of the Hołubla Stream (sites 3-7), the bottom substrate mostly comprised pebbles and cobbles (sites 3-6), or cobbles, gravel, and sand (site 7). Under dry conditions, water formed a chain of isolated pools. At sites 3 and 4, pools were up to 60 cm in depth, and at sites 5 and 6, there were several more extensive pools (4-8 m in length) with deeper water (up to 80 cm). • In the downstream course of the Hołubla Stream (sites 8-10), stones dominated the bottom substrate. • Sites 9 and 10 were located within the San River alluvia (Fig. 1).
• Under dry conditions, stream at site 8 and 9 most often dried up, or isolated pools remained, and at site 10, the stream reach was usually completely dry for several weeks (Table A5).

Hydrological continuity index
• indirectly characterises the possibility of fish movement at the stream reach at a given site. • range 0-2 • was assessed when the fish were sampled.
• in the absence of water or the presence of isolated pools (separated by dry riffles and runs) at the site, the HCI value was '0'. • for a strip of water with a depth not exceeding 2 cm in the riffles and runs, the HCI value was '1'. • when there was more flowing water, the HCI value was '2'.

DRI
Dryness index • Data were collected from each site at the time of sampling • the value '1' was assigned for the presence of water at the stream reach • for a completely dry stream bed, the assigned value was '0'.

Hydrological stability index
• To estimate the HSI, two half years were considered.
• The flow conditions (the higher flow period) were December-May • The dry conditions (the low flow period) were June-November.
• HSI defined the duration in a given year of the study (counted in weeks for each sampling site) when water was absent in the stream reach.

a)
PERMA NOVA • A highly appropriate measure for most ecological data (being counts or other measures of abundance of species), as they often tend to be overdispersed, with heavily right-skewed distributions and a plethora of zeros. In addition, the number of variables (usually species or taxa) often far exceeds the number of sampling units, making traditional statistical approaches either problematic or impossible. • The methods in PERMANOVA allow multivariate data to be modelled, analysed, and tested based on any resemblance measure of choice, and all tests of hypotheses are performed using permutation techniques (Anderson et al. 2008).

b) SIMPER
• Was run to identify fish species/classes that are most likely to account for the similarities within groups, i.e., GrU: UPSTREAM sites, in both seasons, in the AFTER period; GrD1: DOWNSTREAM sites, in the DRY season, in both periods; and GrD2: DOWNSTREAM sites in the WET season, in both periods. • The percentages of each fish species/class in the Bray-Curtis similarity index within the group of sites a were determined. These values indicated the species that were characteristic to each site group. The typical species in a site group were identified using samples acquired from a site with constant abundance and a high ratio of similarity contribution (AvSim) to SD (AvSim/SD) for that site (Clarke and Gorley, 2015).

c) Shade plots
• Shade plots prepared for the 10 Sites × Period combinations (x-axis) and 21 species/classes (y-axis) are shown, separately for WET and DRY seasons.
• Shade plots have the capacity not only to identify common patterns in groups of taxa which appear to be determining sample group structures (as an adjunct to categorical, similarity-based tools such as SIMPER (Clarke, 1993)), but also to interpret continuous multivariate assemblage changes at the level of individual species (Clarke et al., 2014).

d) CCA
• The analysis was performed on the AFTER barrier removal data, as this factor would hinder the correct assessment of the impact of other environmental factors. The analyses included samples from sites where fish appeared at least once. Young cyprinid fish (CYP) occurring in the lower section of the Hołubla Stream, belonging to the species associated with the mainstem rivers, for the CCA analysis were summed up into one category (i.e., CYP-JV+YY). • Eighteen environmental variables were initially considered for investigation; however, their number was reduced to avoid multicollinearity. Pearson's correlation coefficients were calculated for all pairs of environmental variables to identify the sources of redundancy. • Ultimately, six variables (i.e., distance from the mouth, pebbles, water temperature, pools, discharge, and HCI) were used. Species/classes that appeared in less than 5% of the samples were removed from the set (Arrington and Winemiller, 2003). • The collected data was first analysed through gradient length calculations using detrended canonical correspondence analysis (DCCA). The length of the longest gradient in DCCA was 3.7. Consequently, CCA was applied to assess the dependence of fish abundance on environmental variables (ter Braak and Šmilauer, 2012). • The data were centred and standardised. The percentage of environmental data describing the fraction of substrate were arcsine transformed to ensure that the assumptions of the model were met. • The CCA was conducted using a forward-selection procedure. The significance of the CCA axes in explaining species diversity was determined, as was the significance of the effects of specific variables on model ordering, based on a Monte Carlo test with 999 random permutations. • The importance of environmental variables for fish species is described by the length of the arrows in the CCA biplot. The length of the environmental vector indicates the strength of the correlation, and its direction indicates its relationship with the species. • Fish species plotted in the same direction from the origin as an environmental vector are positively correlated with that variable, and a species plotted in the opposite direction indicates a negative relationship (ter Braak and Šmilauer, 2012).